A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi everyone, not sure if this has been asked before, but is there a way to handle analysis with WGS tumor with WES normal?

What is your expectation here? Limit the WGS tumor to the WES mormal regions? Or some mixed tumor/normal and tumor-only calling?

It's the data that we have been handed over from collaborators... normally I would recommend a mixed of tumor/normal and tumor-only calling. But apparently some variant callers can handle this (mutect? never tried) so I'm wondering if Oncoanalyser can handle it.

No, that's not supported and would require a bit of preprocessing and merging.

It's also going to get fairly complicated for anything beyond a rough merger -- like how to handle SVs that cross between the two comparisons, etc.

I would run the tumor in tumor only mode and then see how/if the small variant caller can be fed the T/N and only use the sage output to filter your small variants, anything else is unlikely to be very useful/a lot of hassle